AMS-BP 0.4.0__py3-none-any.whl → 0.4.3__py3-none-any.whl

AMS_BP/__init__.py

@@ -10,4 +10,4 @@ Last updated: 2024-12-16
 
 """
 
-__version__ = "0.4.0"
+__version__ = "0.4.3"

AMS_BP/gui/README.md

@@ -6,12 +6,12 @@ The AMS-BP GUI provides a user-friendly interface for constructing and validatin
 
 This GUI supports:
 
-A template-based configuration builder for quick setup.
-A visual editor for each simulation parameter block (cells, molecules, fluorophores, lasers, etc.).
-Interactive help sections for each tab.
-Simulation execution using prebuilt configs.
-Napari integration for visualization of resulting microscopy data.
-Packaging of simulation logs for easy sharing.
+- A template-based configuration builder for quick setup.
+- A visual editor for each simulation parameter block (cells, molecules, fluorophores, lasers, etc.).
+- Interactive help sections for each tab.
+- Simulation execution using prebuilt configs.
+- Napari integration for visualization of resulting microscopy data.
+- Packaging of simulation logs for easy sharing.
 
 ## Launching the GUI
 
@@ -23,55 +23,59 @@ run_AMS_BP gui
 ### Main Window
 The main window (MainWindow) acts as the launchpad for:
 
-Configuration Builder — Launches a template selector and opens a full editor.
-Run Simulation from Config — Lets you pick a .toml file and start the simulation.
-Visualize Microscopy Data — Opens TIFF and other images in a Napari viewer.
-Package Logs for Sharing — Archives a run_* folder into a .zip.
+- Configuration Builder — Launches a template selector and opens a full editor.
+- Run Simulation from Config — Lets you pick a .toml file and start the simulation.
+- Visualize Microscopy Data — Opens TIFF and other images in a Napari viewer.
+- Package Logs for Sharing — Archives a run_* folder into a .zip.
+
 #### Configuration Editor
 Once a template is selected, the ConfigEditor is launched. It contains:
 
-A dropdown navigation system replacing traditional tabs.
-A floating tab counter and preview/save buttons.
-A help button per section (reads *.md files from help_docs/).
-Live validation using internal config models (convertconfig.py).
+- A dropdown navigation system replacing traditional tabs.
+- A floating tab counter and preview/save buttons.
+- A help button per section (reads *.md files from help_docs/).
+- Live validation using internal config models (convertconfig.py).
+
 ##### Tabs & Widgets
 Each configuration section is implemented as a modular PyQt widget, including:
 
-GlobalConfigWidget
-CellConfigWidget
-MoleculeConfigWidget
-FluorophoreConfigWidget
-CondensateConfigWidget
-LaserConfigWidget
-ExperimentConfigWidget
-...and more
+- GlobalConfigWidget
+- CellConfigWidget
+- MoleculeConfigWidget
+- FluorophoreConfigWidget
+- CondensateConfigWidget
+- LaserConfigWidget
+- ExperimentConfigWidget
+- ...and more
+
 Each widget supports:
 
-get_data() → Extract validated dictionary data
-set_data(data: dict) → Load existing config into the UI
-validate() → Validate using backend logic
-get_help_path() → Load the corresponding markdown help page
+- get_data() → Extract validated dictionary data
+- set_data(data: dict) → Load existing config into the UI
+- validate() → Validate using backend logic
+- get_help_path() → Load the corresponding markdown help page
 
 ####  Running a Simulation
 
 Once you've completed the config file setup via the GUI:
 
-Click "Preview Configuration TOML" to confirm contents.
-Click "Ready to Save Configuration" and choose a .toml path.
-Return to the main window, click "Run Simulation from Config".
-Simulation will launch in a background thread and print logs to a live window.
-Once done, results will be saved in a run_*/ folder.
+- Click "Preview Configuration TOML" to confirm contents.
+- Click "Ready to Save Configuration" and choose a .toml path.
+- Return to the main window, click "Run Simulation from Config".
+- Simulation will launch in a background thread and print logs to a live window.
+- Once done, results will be saved in a run_*/ folder.
 
 #### Viewing Results
 
-Click "Visualize Microscopy Data (Napari)"
-Select any .tif, .tiff, .nd2, or .zarr file
+- Click "Visualize Microscopy Data (Napari)"
+- Select any .tif, .tiff, .nd2, or .zarr file
+
 The data will be loaded into a new Napari viewer session
 
 #### Packaging Logs
 
 To share or archive a completed simulation:
 
-Click "Package Logs for Sharing".
-Select the run_* folder you want.
-Choose a destination for the .zip file.
+- Click "Package Logs for Sharing".
+- Select the run_* folder you want.
+- Choose a destination for the .zip file.

AMS_BP/gui/configuration_window.py

@@ -2,14 +2,16 @@ from pathlib import Path
 
 import tomli
 import tomlkit
+from PyQt6.QtCore import Qt
 from PyQt6.QtWidgets import (
-    QComboBox,
     QDialog,
     QFileDialog,
     QHBoxLayout,
     QLabel,
+    QListWidget,
     QMessageBox,
     QPushButton,
+    QSizePolicy,
     QStackedWidget,
     QTextEdit,
     QVBoxLayout,
@@ -36,54 +38,63 @@ class ConfigEditor(QWidget):
         super().__init__()
         self.setWindowTitle("Simulation Configuration Editor")
 
-        # Create the main layout for the window
-        layout = QVBoxLayout()
-
-        # Create a horizontal layout for the dropdown and the tab index label
-        dropdown_layout = QHBoxLayout()
-
-        # Add a QLabel for the instruction/title about the dropdown
-        dropdown_title = QLabel(
-            "Use the dropdown below to set the parameters for each tab:"
-        )
-        dropdown_layout.addWidget(dropdown_title)
-
-        # Create a QComboBox (dropdown menu) for selecting tabs
-        self.dropdown = QComboBox()
-        self.dropdown.addItems(
-            [
-                "General",
-                "Global Parameters",
-                "Cell Parameters",
-                "Molecule Parameters",
-                "Condensate Parameters",
-                "Define fluorophores",
-                "Camera Parameters",
-                "PSF Parameters",
-                "Laser Parameters",
-                "Channels Parameters",
-                "Saving Instructions",
-                "Experiment Builder",
-            ]
+        # === Main horizontal layout: [Side Navigation | Content Area] ===
+        main_layout = QHBoxLayout(self)
+
+        # === Sidebar: Section Navigation ===
+        self.nav_list = QListWidget()
+        self.sections = [
+            "General",
+            "Global Parameters",
+            "Cell Parameters",
+            "Molecule Parameters",
+            "Condensate Parameters",
+            "Define fluorophores",
+            "Camera Parameters",
+            "PSF Parameters",
+            "Laser Parameters",
+            "Channels Parameters",
+            "Saving Instructions",
+            "Experiment Builder",
+        ]
+        self.nav_list.addItems(self.sections)
+        self.nav_list.setFixedWidth(220)
+        self.nav_list.setSpacing(4)
+        self.nav_list.setCurrentRow(0)
+        self.nav_list.currentRowChanged.connect(self.on_tab_selected)
+        main_layout.addWidget(self.nav_list)
+
+        # === Right panel layout ===
+        right_panel = QVBoxLayout()
+
+        # Step/breadcrumb label
+        self.step_label = QLabel()
+        self.step_label.setAlignment(Qt.AlignmentFlag.AlignLeft)
+        right_panel.addWidget(self.step_label)
+
+        # === Stack of config widgets ===
+        self.stacked_widget = QStackedWidget()
+        self.stacked_widget.setSizePolicy(
+            QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding
         )
-        self.dropdown.currentIndexChanged.connect(
-            self.on_dropdown_change
-        )  # Connect to the change event
+        right_panel.addWidget(self.stacked_widget)
 
-        # Create a QLabel for displaying the current tab index
-        self.tab_index_label = QLabel("1/10")
+        # === Buttons at the bottom ===
+        self.save_button = QPushButton("Ready to save configuration?")
+        self.save_button.clicked.connect(self.save_config)
+        right_panel.addWidget(self.save_button)
 
-        # Add the dropdown and label to the layout
-        dropdown_layout.addWidget(self.dropdown)
-        dropdown_layout.addWidget(self.tab_index_label)
+        self.preview_button = QPushButton("Preview Configuration TOML")
+        self.preview_button.clicked.connect(self.preview_config)
+        right_panel.addWidget(self.preview_button)
 
-        # Add the dropdown layout to the main layout
-        layout.addLayout(dropdown_layout)
+        self.help_button = QPushButton("Get Help on this section")
+        self.help_button.clicked.connect(self.show_help)
+        right_panel.addWidget(self.help_button)
 
-        # Create a QStackedWidget to hold the content for each "tab"
-        self.stacked_widget = QStackedWidget()
+        main_layout.addLayout(right_panel)
 
-        # Initialize the widgets for each "tab"
+        # === Create tab content widgets ===
         self.general_tab = GeneralConfigWidget()
         self.global_tab = GlobalConfigWidget()
         self.cell_tab = CellConfigWidget()
@@ -97,36 +108,35 @@ class ConfigEditor(QWidget):
         self.detector_tab = CameraConfigWidget()
         self.experiment_tab = ExperimentConfigWidget()
 
-        # connections
-        # PSF -> confocal -> lasers
+        # === Widget interconnections ===
         self.psf_tab.confocal_mode_changed.connect(self.laser_tab.set_confocal_mode)
-        # === Molecule -> Fluorophore & Condensate ===
+
         self.molecule_tab.molecule_count_changed.connect(
             self.fluorophore_tab.set_mfluorophore_count
         )
         self.molecule_tab.molecule_count_changed.connect(
             self.condensate_tab.set_molecule_count
         )
-        # === Fluorophore -> Molecule & Condensate ===
+
         self.fluorophore_tab.mfluorophore_count_changed.connect(
             self.molecule_tab.set_molecule_count
         )
         self.fluorophore_tab.mfluorophore_count_changed.connect(
             self.condensate_tab.set_molecule_count
         )
-        # === Condensate -> Molecule & Fluorophore ===
+
         self.condensate_tab.molecule_count_changed.connect(
             self.molecule_tab.set_molecule_count
         )
         self.condensate_tab.molecule_count_changed.connect(
             self.fluorophore_tab.set_mfluorophore_count
         )
-        # === Laser -> Experiment
+
         self.laser_tab.laser_names_updated.connect(
             self.experiment_tab.set_active_lasers
         )
 
-        # Add each tab's widget to the stacked widget
+        # === Add tab widgets to the stack ===
         self.stacked_widget.addWidget(self.general_tab)
         self.stacked_widget.addWidget(self.global_tab)
         self.stacked_widget.addWidget(self.cell_tab)
@@ -140,27 +150,13 @@ class ConfigEditor(QWidget):
         self.stacked_widget.addWidget(self.output_tab)
         self.stacked_widget.addWidget(self.experiment_tab)
 
-        # Set the stacked widget as the central widget
-        layout.addWidget(self.stacked_widget)
-
-        # Create and add the save and help buttons at the bottom
-        self.save_button = QPushButton("Ready to save configuration?")
-        self.save_button.clicked.connect(self.save_config)
-        layout.addWidget(self.save_button)
-
-        self.preview_button = QPushButton("Preview Configuration TOML")
-        self.preview_button.clicked.connect(self.preview_config)
-        layout.addWidget(self.preview_button)
-
-        self.help_button = QPushButton("Get Help on this section")
-        self.help_button.clicked.connect(self.show_help)
-        layout.addWidget(self.help_button)
-
-        # Set the layout for the main window
-        self.setLayout(layout)
+        # Final layout and window size
+        self.setLayout(main_layout)
+        self.setMinimumSize(1100, 750)
+        self.resize(1250, 850)
 
-        # Set initial display
-        self.on_dropdown_change(0)  # Show the first tab (index 0)
+        # Initial tab display
+        self.on_tab_selected(0)
 
     def set_data(self, config: dict):
         if "Cell_Parameters" in config:
@@ -236,14 +232,12 @@ class ConfigEditor(QWidget):
             doc[key] = val
         return doc
 
-    def on_dropdown_change(self, index):
-        """Change the displayed widget based on the dropdown selection."""
+    def on_tab_selected(self, index: int):
+        """Change the displayed widget and update breadcrumb/step label."""
         self.stacked_widget.setCurrentIndex(index)
-        # Update the tab index label (1-based index)
-        total_tabs = (
-            self.dropdown.count()
-        )  # Corrected way to get the total number of items
-        self.tab_index_label.setText(f"{index + 1}/{total_tabs}")
+        total = self.nav_list.count()
+        current = self.nav_list.item(index).text()
+        self.step_label.setText(f"Step {index + 1}/{total} — {current}")
 
     def validate_all_tabs(self) -> bool:
         return all(

AMS_BP/gui/main.py

@@ -4,10 +4,11 @@ from zipfile import ZipFile
 
 import napari
 import tifffile
-from PyQt6.QtCore import Qt, QThread
+from PyQt6.QtCore import QSettings, Qt, QThread
 from PyQt6.QtGui import QPainter, QPixmap
 from PyQt6.QtSvg import QSvgRenderer
 from PyQt6.QtWidgets import (
+    QApplication,
     QFileDialog,
     QLabel,
     QMainWindow,
@@ -22,6 +23,7 @@ from ..logging.setup_run_directory import setup_run_directory
 from .logging_window import LogWindow
 from .sim_worker import SimulationWorker
 from .template_window_selection import TemplateSelectionWindow
+from .widgets.utility_widgets.toggleswitch_widget import ToggleSwitch
 
 LOGO_PATH = str(Path(__file__).parent / "assets" / "drawing.svg")
 
@@ -77,6 +79,20 @@ class MainWindow(QMainWindow):
         self.package_logs_button.clicked.connect(self.package_logs)
         layout.addWidget(self.package_logs_button)
 
+        # Load theme preference
+        self.settings = QSettings("AMS", "AMSConfig")
+        theme_pref = self.settings.value("theme", "light")
+
+        # Add toggle switch with label
+        self.theme_toggle = ToggleSwitch(checked=(theme_pref == "dark"))
+        self.theme_toggle.toggled.connect(self.toggle_theme)
+        self.theme_label = QLabel("Dark Mode" if theme_pref == "dark" else "Light Mode")
+        layout.addWidget(self.theme_label)
+        layout.addWidget(self.theme_toggle, alignment=Qt.AlignmentFlag.AlignCenter)
+
+        # Apply initial theme
+        self.apply_theme(theme_pref)
+
     def package_logs(self):
         log_dir = Path.home() / "AMS_runs"
 
@@ -245,6 +261,21 @@ class MainWindow(QMainWindow):
         else:
             print("Failed to load SVG file.")
 
+    def toggle_theme(self, is_dark: bool):
+        theme = "dark" if is_dark else "light"
+        self.settings.setValue("theme", theme)
+        self.apply_theme(theme)
+        self.theme_label.setText("Dark Mode" if is_dark else "Light Mode")
+
+    def apply_theme(self, theme: str):
+        theme_file = Path(__file__).parent / "themes" / f"{theme}_theme.qss"
+        try:
+            with open(theme_file, "r") as f:
+                stylesheet = f.read()
+                QApplication.instance().setStyleSheet(stylesheet)
+        except Exception as e:
+            QMessageBox.warning(self, "Theme Error", f"Failed to load theme:\n{e}")
+
     def open_config_editor(self):
         """Launch template selection first, then open ConfigEditor."""
         self.template_window = TemplateSelectionWindow()

AMS_BP/gui/themes/dark_theme.qss

@@ -0,0 +1,86 @@
+/* Dark Theme */
+* {
+    font-family: "Segoe UI", "Arial", sans-serif;
+    font-size: 14px;
+    color: #e0e0e0;
+}
+
+QWidget {
+    background-color: #2b2b2b;
+}
+
+QLabel {
+    color: #dddddd;
+}
+
+QPushButton {
+    background-color: #3daee9;
+    color: #ffffff;
+    border-radius: 6px;
+    padding: 6px 12px;
+}
+QPushButton:hover {
+    background-color: #5dbff0;
+}
+QPushButton:pressed {
+    background-color: #2a97cc;
+}
+
+QLineEdit, QComboBox, QSpinBox, QDoubleSpinBox, QTextEdit {
+    background-color: #3c3f41;
+    border: 1px solid #555;
+    border-radius: 4px;
+    padding: 4px;
+    color: #eeeeee;
+}
+
+QGroupBox {
+    border: 1px solid #444;
+    border-radius: 6px;
+    margin-top: 10px;
+}
+QGroupBox:title {
+    subcontrol-origin: margin;
+    subcontrol-position: top left;
+    padding: 0 6px;
+    font-weight: bold;
+    color: #aaaaaa;
+}
+
+QTabWidget::pane {
+    border: 1px solid #444;
+    background: #3c3f41;
+    border-radius: 6px;
+}
+
+QTabBar::tab {
+    background: #444;
+    border: 1px solid #555;
+    padding: 6px 12px;
+    border-top-left-radius: 6px;
+    border-top-right-radius: 6px;
+}
+QTabBar::tab:selected {
+    background: #2b2b2b;
+    border-bottom-color: #2b2b2b;
+}
+
+QScrollArea {
+    border: none;
+}
+
+QListWidget {
+    background-color: #2f2f2f;
+    border-right: 1px solid #444;
+}
+
+QListWidget::item {
+    padding: 6px;
+    border-radius: 4px;
+    color: #dddddd;
+}
+
+QListWidget::item:selected {
+    background-color: #3daee9;
+    color: #ffffff;
+}

AMS_BP/gui/themes/light_theme.qss

@@ -0,0 +1,85 @@
+/* Light Theme */
+* {
+    font-family: "Segoe UI", "Arial", sans-serif;
+    font-size: 14px;
+    color: #2b2b2b;
+}
+
+QWidget {
+    background-color: #f5f7fa;
+}
+
+QLabel {
+    color: #333;
+}
+
+QPushButton {
+    background-color: #007acc;
+    color: white;
+    border-radius: 6px;
+    padding: 6px 12px;
+}
+QPushButton:hover {
+    background-color: #005f9e;
+}
+QPushButton:pressed {
+    background-color: #004d80;
+}
+
+QLineEdit, QComboBox, QSpinBox, QDoubleSpinBox, QTextEdit {
+    background-color: white;
+    border: 1px solid #ccc;
+    border-radius: 4px;
+    padding: 4px;
+}
+
+QGroupBox {
+    border: 1px solid #d6d9dc;
+    border-radius: 6px;
+    margin-top: 10px;
+}
+QGroupBox:title {
+    subcontrol-origin: margin;
+    subcontrol-position: top left;
+    padding: 0 6px;
+    font-weight: bold;
+    color: #555;
+}
+
+QTabWidget::pane {
+    border: 1px solid #d1dbe3;
+    background: #ffffff;
+    border-radius: 6px;
+}
+
+QTabBar::tab {
+    background: #e6ebf1;
+    border: 1px solid #cfd7df;
+    padding: 6px 12px;
+    border-top-left-radius: 6px;
+    border-top-right-radius: 6px;
+}
+QTabBar::tab:selected {
+    background: #ffffff;
+    border-bottom-color: #ffffff;
+}
+
+QScrollArea {
+    border: none;
+}
+
+QListWidget {
+    background-color: #f0f0f0;
+    border-right: 1px solid #ccc;
+}
+
+QListWidget::item {
+    padding: 6px;
+    border-radius: 4px;
+}
+
+QListWidget::item:selected {
+    background-color: #007acc;
+    color: white;
+}
+

AMS_BP/gui/widgets/camera_config_widget.py

@@ -8,6 +8,7 @@ from PyQt6.QtWidgets import (
     QHBoxLayout,
     QMessageBox,
     QPushButton,
+    QSizePolicy,
     QSpinBox,
     QVBoxLayout,
     QWidget,
@@ -19,12 +20,14 @@ from .utility_widgets.spectrum_widget import SpectrumEditorDialog
 class CameraConfigWidget(QWidget):
     def __init__(self):
         super().__init__()
+
         layout = QVBoxLayout()
-        form = QFormLayout()
+        layout.setContentsMargins(10, 10, 10, 10)
+        layout.setSpacing(10)
+        self.setLayout(layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
 
-        self.validate_button = QPushButton("Validate")
-        self.validate_button.clicked.connect(self.validate)
-        layout.addWidget(self.validate_button)
+        form = QFormLayout()
 
         # Camera type (Only "CMOS" is available)
         self.camera_type = QComboBox()
@@ -89,6 +92,10 @@ class CameraConfigWidget(QWidget):
         layout.addLayout(form)
         self.setLayout(layout)
 
+        self.validate_button = QPushButton("Validate Parameters")
+        self.validate_button.clicked.connect(self.validate)
+        layout.addWidget(self.validate_button)
+
     def _hbox(self, widgets):
         box = QHBoxLayout()
         for w in widgets:

AMS_BP/gui/widgets/cell_config_widget.py

@@ -8,6 +8,7 @@ from PyQt6.QtWidgets import (
     QHBoxLayout,
     QMessageBox,
     QPushButton,
+    QSizePolicy,
     QStackedWidget,
     QVBoxLayout,
     QWidget,
@@ -18,11 +19,12 @@ class CellConfigWidget(QWidget):
     def __init__(self):
         super().__init__()
         layout = QVBoxLayout()
-        form = QFormLayout()
+        layout.setContentsMargins(10, 10, 10, 10)
+        layout.setSpacing(10)
+        self.setLayout(layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
 
-        self.validate_button = QPushButton("Validate")
-        self.validate_button.clicked.connect(self.validate)
-        layout.addWidget(self.validate_button)
+        form = QFormLayout()
 
         self.cell_type = QComboBox()
         self.cell_type.addItems(
@@ -46,6 +48,10 @@ class CellConfigWidget(QWidget):
         layout.addWidget(self.param_stack)
         self.setLayout(layout)
 
+        self.validate_button = QPushButton("Validate Parameters")
+        self.validate_button.clicked.connect(self.validate)
+        layout.addWidget(self.validate_button)
+
     def validate(self) -> bool:
         from ...cells import create_cell
         from ...configio.configmodels import CellParameters

AMS_BP/gui/widgets/channel_config_widget.py

@@ -8,6 +8,7 @@ from PyQt6.QtWidgets import (
     QLineEdit,
     QMessageBox,
     QPushButton,
+    QSizePolicy,
     QSpinBox,
     QTabWidget,
     QVBoxLayout,
@@ -21,11 +22,12 @@ class ChannelConfigWidget(QWidget):
         self.channel_widgets = []
 
         layout = QVBoxLayout()
-        form = QFormLayout()
+        layout.setContentsMargins(10, 10, 10, 10)
+        layout.setSpacing(10)
+        self.setLayout(layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
 
-        self.validate_button = QPushButton("Validate")
-        self.validate_button.clicked.connect(self.validate)
-        layout.addWidget(self.validate_button)
+        form = QFormLayout()
 
         self.num_channels = QSpinBox()
         self.num_channels.setRange(1, 10)
@@ -40,6 +42,10 @@ class ChannelConfigWidget(QWidget):
         layout.addWidget(self.channel_tabs)
         self.setLayout(layout)
 
+        self.validate_button = QPushButton("Validate Parameters")
+        self.validate_button.clicked.connect(self.validate)
+        layout.addWidget(self.validate_button)
+
     def validate(self) -> bool:
         try:
             from ...configio.convertconfig import create_channels

AMS_BP/gui/widgets/condensate_config_widget.py

@@ -11,6 +11,7 @@ from PyQt6.QtWidgets import (
     QMessageBox,
     QPushButton,
     QScrollArea,
+    QSizePolicy,
     QSpinBox,
     QTabWidget,
     QVBoxLayout,
@@ -31,6 +32,10 @@ class CondensateConfigWidget(QWidget):
 
     def setup_ui(self):
         layout = QVBoxLayout()
+        layout.setContentsMargins(10, 10, 10, 10)
+        layout.setSpacing(10)
+        self.setLayout(layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
 
         # Instructions label
         instructions = QLabel(
@@ -113,6 +118,18 @@ class CondensateConfigWidget(QWidget):
         condensate_controls.addWidget(condensate_count)
         layout.addLayout(condensate_controls)
 
+        # === Density Difference field RIGHT AFTER the condensate count ===
+        density_layout = QHBoxLayout()
+        density_layout.addWidget(QLabel("Density Difference:"))
+
+        density_spin = QDoubleSpinBox()
+        density_spin.setRange(0, 100)
+        density_spin.setValue(1.0)
+        density_spin.setDecimals(3)
+        density_layout.addWidget(density_spin)
+        layout.addLayout(density_layout)
+
+        # === Condensate containers BELOW this point ===
         condensate_container = QVBoxLayout()
         layout.addLayout(condensate_container)
 
@@ -126,25 +143,16 @@ class CondensateConfigWidget(QWidget):
             )
         )
 
-        # Density Difference per molecule type
-        density_layout = QHBoxLayout()
-        density_layout.addWidget(QLabel("Density Difference:"))
-
-        density_spin = QDoubleSpinBox()
-        density_spin.setRange(0, 100)
-        density_spin.setValue(1.0)
-        density_spin.setDecimals(3)
-        density_layout.addWidget(density_spin)
-        layout.addLayout(density_layout)
         self.condensate_widgets.append(
             {
                 "condensates": condensate_widgets,
                 "density_widget": density_spin,
+                "condensate_count_spinner": condensate_count,
             }
         )
+
         molecule_widget.setLayout(layout)
         scroll_area.setWidget(molecule_widget)
-
         self.tab_widget.addTab(scroll_area, f"Molecule Type {index + 1}")
 
     def add_condensate_group(self, index, condensate_widgets, condensate_container):
@@ -242,6 +250,7 @@ class CondensateConfigWidget(QWidget):
                 molecule_group["condensates"],
                 molecule_group_layout,
             )
+            molecule_group["condensate_count_spinner"].setValue(num_condensates)
 
             for j in range(num_condensates):
                 condensate = molecule_group["condensates"][j]

AMS_BP/gui/widgets/experiment_config_widget.py

@@ -10,6 +10,8 @@ from PyQt6.QtWidgets import (
     QLineEdit,
     QMessageBox,
     QPushButton,
+    QScrollArea,
+    QSizePolicy,
     QSpinBox,
     QTabWidget,
     QVBoxLayout,
@@ -25,6 +27,10 @@ class ExperimentConfigWidget(QWidget):
         self.laser_position_widgets = {}
 
         layout = QVBoxLayout()
+        layout.setContentsMargins(10, 10, 10, 10)
+        layout.setSpacing(10)
+        self.setLayout(layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
         form = QFormLayout()
 
         # Experiment Info
@@ -38,13 +44,20 @@ class ExperimentConfigWidget(QWidget):
         self.type_field.addItems(["time-series", "z-stack"])
         form.addRow("Experiment Type:", self.type_field)
 
-        # Z Position (just one for time-series)
+        # Z Position inputs
         self.z_position_inputs: List[QDoubleSpinBox] = []
 
+        # Scrollable container for z-position inputs
+        self.z_scroll_area = QScrollArea()
+        self.z_scroll_area.setWidgetResizable(True)
+        self.z_scroll_area.setFixedHeight(150)  # Adjust height as needed
+
         self.z_position_container = QWidget()
-        self.z_position_layout = QVBoxLayout()
+        self.z_position_layout = QVBoxLayout(self.z_position_container)
         self.z_position_container.setLayout(self.z_position_layout)
-        form.addRow("Z Position(s):", self.z_position_container)
+
+        self.z_scroll_area.setWidget(self.z_position_container)
+        form.addRow("Z Position(s):", self.z_scroll_area)
 
         self.add_z_button = QPushButton("Add Z-Position")
         self.remove_z_button = QPushButton("Remove Z-Position")
@@ -83,13 +96,13 @@ class ExperimentConfigWidget(QWidget):
         layout.addWidget(QLabel("Active Laser Parameters:"))
         layout.addWidget(self.laser_tabs)
 
+        self.setLayout(layout)
+
         # Validate Button
-        self.validate_button = QPushButton("Validate")
+        self.validate_button = QPushButton("Validate Parameters")
         self.validate_button.clicked.connect(self.validate)
         layout.addWidget(self.validate_button)
 
-        self.setLayout(layout)
-
     def update_z_position_mode(self, mode: str):
         # Clear existing
         for i in reversed(range(self.z_position_layout.count())):

AMS_BP/gui/widgets/flurophore_config_widget.py

@@ -11,6 +11,7 @@ from PyQt6.QtWidgets import (
     QMessageBox,
     QPushButton,
     QScrollArea,
+    QSizePolicy,
     QSpinBox,
     QTabWidget,
     QVBoxLayout,
@@ -33,6 +34,10 @@ class FluorophoreConfigWidget(QWidget):
 
     def setup_ui(self):
         layout = QVBoxLayout()
+        layout.setContentsMargins(10, 10, 10, 10)
+        layout.setSpacing(10)
+        self.setLayout(layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
 
         instructions = QLabel(
             "Configure fluorophores and their respective states and transitions."

AMS_BP/gui/widgets/global_config_widget.py

@@ -5,6 +5,7 @@ from PyQt6.QtWidgets import (
     QHBoxLayout,
     QMessageBox,
     QPushButton,
+    QSizePolicy,
     QSpinBox,
     QVBoxLayout,
     QWidget,
@@ -18,11 +19,12 @@ class GlobalConfigWidget(QWidget):
 
     def setup_ui(self):
         layout = QVBoxLayout()
+        layout.setContentsMargins(10, 10, 10, 10)
+        layout.setSpacing(10)
+        self.setLayout(layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
+
         form = QFormLayout()
-        # Validation button
-        self.validate_button = QPushButton("Validate Parameters")
-        self.validate_button.clicked.connect(self.validate)
-        layout.addWidget(self.validate_button)
 
         # Sample plane dimensions
         self.sample_plane_width = QSpinBox()
@@ -71,6 +73,11 @@ class GlobalConfigWidget(QWidget):
 
         self.setLayout(layout)
 
+        # Validation button
+        self.validate_button = QPushButton("Validate Parameters")
+        self.validate_button.clicked.connect(self.validate)
+        layout.addWidget(self.validate_button)
+
     def set_defaults(self):
         """Set default values for the form fields"""
         self.sample_plane_width.setValue(50)  # 1000 μm

AMS_BP/gui/widgets/laser_config_widget.py

@@ -8,6 +8,7 @@ from PyQt6.QtWidgets import (
     QLineEdit,
     QMessageBox,
     QPushButton,
+    QSizePolicy,
     QSpinBox,
     QTabWidget,
     QVBoxLayout,
@@ -22,11 +23,12 @@ class LaserConfigWidget(QWidget):
         super().__init__()
         self.laser_name_widgets = []
         layout = QVBoxLayout()
-        form = QFormLayout()
+        layout.setContentsMargins(10, 10, 10, 10)
+        layout.setSpacing(10)
+        self.setLayout(layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
 
-        self.validate_button = QPushButton("Validate")
-        self.validate_button.clicked.connect(self.validate)
-        layout.addWidget(self.validate_button)
+        form = QFormLayout()
 
         self.num_lasers = QSpinBox()
         self.num_lasers.setRange(1, 10)
@@ -44,6 +46,10 @@ class LaserConfigWidget(QWidget):
         layout.addWidget(self.laser_tabs)
         self.setLayout(layout)
 
+        self.validate_button = QPushButton("Validate Parameters")
+        self.validate_button.clicked.connect(self.validate)
+        layout.addWidget(self.validate_button)
+
     def set_confocal_mode(self, enabled: bool):
         for i in range(self.laser_tabs.count()):
             tab = self.laser_tabs.widget(i)

AMS_BP/gui/widgets/molecule_config_widget.py

@@ -13,6 +13,7 @@ from PyQt6.QtWidgets import (
     QMessageBox,
     QPushButton,
     QScrollArea,
+    QSizePolicy,
     QSpinBox,
     QTabWidget,
     QVBoxLayout,
@@ -28,6 +29,11 @@ class MoleculeConfigWidget(QWidget):
         super().__init__()
 
         self.main_layout = QVBoxLayout()
+        self.main_layout.setContentsMargins(10, 10, 10, 10)
+        self.main_layout.setSpacing(10)
+        self.setLayout(self.main_layout)
+        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
+
         self.setLayout(self.main_layout)
 
         # Number of molecule types spinner
@@ -41,11 +47,6 @@ class MoleculeConfigWidget(QWidget):
         self.num_types_layout.addWidget(self.num_types_spinner)
         self.num_types_layout.addStretch()
 
-        # Validate button
-        self.validate_button = QPushButton("Validate")
-        self.validate_button.clicked.connect(self.validate)
-        self.num_types_layout.addWidget(self.validate_button)
-
         self.main_layout.addLayout(self.num_types_layout)
 
         # Create tab widget to hold molecule type configs
@@ -56,6 +57,11 @@ class MoleculeConfigWidget(QWidget):
         self.molecule_type_widgets = []
         self.update_molecule_types(1)
 
+        # Add the validate button at the bottom
+        self.validate_button = QPushButton("Validate Parameters")
+        self.validate_button.clicked.connect(self.validate)
+        self.main_layout.addWidget(self.validate_button)
+
     def _on_molecule_count_changed(self, count):
         self.update_molecule_types(count)
         self.molecule_count_changed.emit(count)
@@ -235,6 +241,9 @@ class MoleculeConfigWidget(QWidget):
             }
             self.molecule_type_widgets[i].set_data(type_data)
 
+    def get_help_path(self) -> Path:
+        return Path(__file__).parent.parent / "help_docs" / "molecule_help.md"
+
 
 class MoleculeTypeWidget(QWidget):
     def __init__(self, type_index):
@@ -709,6 +718,3 @@ class TransitionMatrixWidget(QWidget):
         for i in range(size):
             for j in range(min(size, len(matrix[i]))):
                 self.spinboxes[i][j].setValue(matrix[i][j])
-
-    def get_help_path(self) -> Path:
-        return Path(__file__).parent.parent / "help_docs" / "molecule_help.md"

AMS_BP/gui/widgets/utility_widgets/toggleswitch_widget.py

@@ -0,0 +1,60 @@
+from PyQt6.QtCore import QPropertyAnimation, QSize, Qt, pyqtSignal
+from PyQt6.QtGui import QBrush, QColor, QPainter
+from PyQt6.QtWidgets import QWidget
+
+
+class ToggleSwitch(QWidget):
+    toggled = pyqtSignal(bool)
+
+    def __init__(self, parent=None, checked=False):
+        super().__init__(parent)
+        self.setFixedSize(50, 28)
+        self._checked = checked
+        self._circle_position = 2 if not checked else 24
+
+        self.animation = QPropertyAnimation(self, b"")
+        self.animation.setDuration(200)
+
+    def sizeHint(self):
+        return QSize(50, 28)
+
+    def mousePressEvent(self, event):
+        self._checked = not self._checked
+        self.animate_toggle()
+        self.toggled.emit(self._checked)
+        self.update()
+
+    def animate_toggle(self):
+        start = self._circle_position
+        end = 24 if self._checked else 2
+        self.animation.stop()
+        self.animation.setStartValue(start)
+        self.animation.setEndValue(end)
+        self.animation.valueChanged.connect(self.set_circle_position)
+        self.animation.start()
+
+    def set_circle_position(self, val):
+        self._circle_position = val
+        self.update()
+
+    def paintEvent(self, event):
+        painter = QPainter(self)
+        painter.setRenderHint(QPainter.RenderHint.Antialiasing)
+
+        # NEW: Background indicates *next* theme
+        bg_color = QColor("#dddddd") if self._checked else QColor("#333333")
+        painter.setBrush(QBrush(bg_color))
+        painter.setPen(Qt.PenStyle.NoPen)
+        painter.drawRoundedRect(0, 0, self.width(), self.height(), 14, 14)
+
+        # Handle (always green)
+        painter.setBrush(QBrush(QColor("#008000")))
+        painter.drawEllipse(int(self._circle_position), 2, 24, 24)
+
+    def isChecked(self):
+        return self._checked
+
+    def setChecked(self, checked: bool):
+        self._checked = checked
+        self._circle_position = 24 if checked else 2
+        self.update()

{ams_bp-0.4.0.dist-info → ams_bp-0.4.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.4.0
+Version: 0.4.3
 Summary: Advanced Microscopy Simulations developed for the Weber Lab by Baljyot Singh Parmar
 Project-URL: Documentation, https://joemans3.github.io/AMS_BP/
 Project-URL: Source code, https://github.com/joemans3/AMS_BP
@@ -46,7 +46,7 @@ Find detailed API references for the library at: [joemans3/github.io/AMS_BP](htt
 
 > !!ATTENTION!! - Please note that you NEED to install the developmental dependencies to run the examples in full. This is mainly for installing the Jupyter notebook extensions, matplotlib and other visualization packages.
 
-[<img src="./docs/assets/buttons/ButtonFigure_FRAP.svg" width="300" height="120"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_fPALM_NPC.svg" width="300"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb)
+[<img src="./docs/assets/buttons/ButtonFigure_FRAP.svg" width="300" height="120"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_fPALM_NPC.svg" width="300"/>](./examples/QuantitativeExperiments/PALM/fPALM/npc_palm.ipynb)
 
 [<img src="./docs/assets/buttons/ButtonFigure_zstack_twocolor_widefield.svg" width="300"/>](./examples/QuantitativeExperiments/TwoColor/Widefield/widefield_twocolor.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_zstack_twocolor_confocal.svg" width="300"/>](./examples/QuantitativeExperiments/TwoColor/Confocal/confocal_twocolor.ipynb)
 
@@ -63,31 +63,29 @@ Find detailed API references for the library at: [joemans3/github.io/AMS_BP](htt
 
 
 ### ***Installing the CLI tool using UV***
-
-
-
-
 1. [Install UV](https://docs.astral.sh/uv/getting-started/installation/).
 2. Run the command:
 ```bash
 uv tool install AMS_BP
 ```
-3. You will have access to two CLI commands (using the uv interface):
+3. You will have access to three CLI commands (using the uv interface):
     - `run_AMS_BP runsim` : This is the main entry point for the simulation. (see `run_AMS_BP runsim --help` for more details)
     - `run_AMS_BP config` : This is a helper tool to generate a template config file for the simulation. (see `run_AMS_BP config --help` for more details)
+    - `run_AMS_BP gui` : to start the GUI. See [GUI Documentation](./src/AMS_BP/gui/README.md)
     - Note: using `run_AMS_BP --help` will show you all the available commands.
 4. You can now use these tools (they are isolated in their own env created by uv, which is cool).
 
 ### ***PyPi***
 
-1. Run:
+1. If using pip, make sure the environment is python >= 3.12
+2. Run:
 ```bash
 pip install AMS_BP
 ```
 
 ## Command Line Interface
 
-AMS-BP provides a command-line interface with two main commands:
+AMS-BP provides a command-line interface with three main commands:
 
 ```bash
 # Generate a default configuration file
@@ -111,10 +109,10 @@ In addition to the CLI and programmatic API, AMS-BP comes with a graphical inter
 ### Main GUI Features
 The GUI provides the following tools from a single interface:
 
-**Create Configuration File** — Launches the visual configuration builder
-**Run Simulation from Config** — Select a .toml file and run the simulation with logging and progress tracking
-**Visualize Microscopy Data (Napari)** — Open TIFF, PNG, ND2, or Zarr image files and view with the Napari viewer
-**Package Logs for Sharing** — Package run directories (e.g., run_2024_04_20_001) into a .zip file for archival or collaboration
+- **Create Configuration File** — Launches the visual configuration builder
+- **Run Simulation from Config** — Select a .toml file and run the simulation with logging and progress tracking
+- **Visualize Microscopy Data (Napari)** — Open TIFF, PNG, ND2, or Zarr image files and view with the Napari viewer
+- **Package Logs for Sharing** — Package run directories (e.g., run_2024_04_20_001) into a .zip file for archival or collaboration
 
 ### Launch the GUI
 To start the GUI, run:
@@ -123,23 +121,7 @@ To start the GUI, run:
 
 run_AMS_BP gui
 ```
-#### Configuration Builder
-Clicking "Create Configuration File" opens a template selector where you can choose a preconfigured simulation (with preview images), and then visually edit all configuration options through dedicated tabs.
-
-Each section of the configuration is editable via structured UI forms, with contextual help and validation. Tabs include:
-
-- Global/Cell/Molecule/Condensate/Fluorophore parameters
-- Laser and optical configuration
-- Camera and channel settings
-- Experiment setup (e.g., z-stack vs time-series)
-Once ready, click "Preview Configuration TOML" to inspect the final file, and "Save" to export.
-
-#### Running Simulations from GUI
-Clicking "Run Simulation from Config" lets you select any .toml configuration file. A real-time log viewer shows progress, and outputs are saved in a structured AMS_runs/run_*/ directory.
-
-#### Sharing Logs
-Run into an issue? Use the packge logs button to select the logs corresponding to the simulation you just ran, save them and send them over to us! It will help you diagnose the issue!
-
+For detailed walkthrough see the [GUI Documentation](./src/AMS_BP/gui/README.md).
 ## Configuration File
 
 The configuration file (sim_config.toml) is divided into several key sections:

{ams_bp-0.4.0.dist-info → ams_bp-0.4.3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-AMS_BP/__init__.py,sha256=vbGheVo9C5jwfrzQFJLyewPR1WvcABOu4ccX4_K3ptw,326
+AMS_BP/__init__.py,sha256=HU_BdGVyL7jcOOv7vIsvzAcl1MzpHKqDjt9B36Nrd0g,326
 AMS_BP/main_cli.py,sha256=DpRzWDsmI0nJvrzJj58F9k1k5ShSj8pCT7N0oH-_8BU,5786
 AMS_BP/run_sim_util.py,sha256=UQr0l9rbtTmzuuWXjkIaTQV-ETO5AqyXRwflF6U2WYs,2415
 AMS_BP/sim_config.toml,sha256=G0wW9qsxciZA1Y0Zm6YgZ00ZDBEBBLw_XXq4gsVRjSY,11778
@@ -13,12 +13,12 @@ AMS_BP/configio/experiments.py,sha256=HdfaSi0gPPJ_wLF87XcW5ICja19Uezx7-ygFEwNzi3
 AMS_BP/configio/saving.py,sha256=596QgAadV32rzsN4B2FngGFcBWCzCDnLFN-qtQsv3bM,857
 AMS_BP/groundtruth_generators/__init__.py,sha256=UPVmhiB81OfyqAes5LoN-n6XgQuBCYCqRPAGd2jpMfc,99
 AMS_BP/groundtruth_generators/nuclearporecomplexes.py,sha256=1aBcWltsKo0OGd7A9GfuEZ3azQBx5SzpjrSLLMXuYn8,2518
-AMS_BP/gui/README.md,sha256=VGhzOkGFhMfhwDyU0hkAyIV6I4t_JEdYq19YyTaUato,2702
+AMS_BP/gui/README.md,sha256=z2XreAPQeeFmKSXbhsa2kznHbk-YbLD55-VPWikNQp4,2778
 AMS_BP/gui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-AMS_BP/gui/configuration_window.py,sha256=d-eEz099-LWSn0_O8ZKn1425jkMAxoAFW4-BZ3qW90c,12606
+AMS_BP/gui/configuration_window.py,sha256=BNlJvwKKAVPMh7cXxOSl9DGvWVwSc6sPwLlZAGGdGes,12101
 AMS_BP/gui/help_window.py,sha256=Jn844Vez7ULC1VGKb4iGgRvuw3wPTd0pcyRv7VWbeV4,790
 AMS_BP/gui/logging_window.py,sha256=a7HbmfYP3YavLuyT317YRE1xWXJtB4i8EoK9QAstOv8,2938
-AMS_BP/gui/main.py,sha256=VE8jPgWyuGSXTnux-en0BEFWc9D9shrwFDvtzSLcfpI,9311
+AMS_BP/gui/main.py,sha256=O2FPkyIjCcEbn3dPBefowXQx4kfuB1oUkTyIDI5Me8M,10653
 AMS_BP/gui/sim_worker.py,sha256=SYKbHGQNd9laL2YMjPfm755eRTyub434fSTQ5mGS9iM,1989
 AMS_BP/gui/template_window_selection.py,sha256=GgLfApuTa4qNiek0Ksiqy15aqhdOIZyaReFYAS9NDoc,3034
 AMS_BP/gui/assets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -36,22 +36,25 @@ AMS_BP/gui/help_docs/laser_help.md,sha256=wzloXV_1WCT6zRTrf1jKC-cMlepntacZV7jbLL
 AMS_BP/gui/help_docs/molecule_help.md,sha256=5wnyNlCTWjCsgwzRFG7XhnlGXao6qXj-2ZL0yfnHQng,2793
 AMS_BP/gui/help_docs/output_help.md,sha256=Rg0dV0N4ClrJvPTt5HaJHuQgHE5nmgKwiQCAHhV0A24,225
 AMS_BP/gui/help_docs/psf_help.md,sha256=onH-suSxocfj9mD6WCE6lG7yxov1yCoGeau82oG-zmo,1854
+AMS_BP/gui/themes/dark_theme.qss,sha256=6MUyaaZnmZCnXTNNJuqi7NN8Om8P8P9pSfAffv4ampA,1462
+AMS_BP/gui/themes/light_theme.qss,sha256=wVEIcnFzGVZN7ohLHrus6zX5ybGnyfTwihAPSvhrDL8,1424
 AMS_BP/gui/widgets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-AMS_BP/gui/widgets/camera_config_widget.py,sha256=hp1fyRH3kVmQK5HVyoli1RAat8dERq8bjnXjRK8qGVA,7559
-AMS_BP/gui/widgets/cell_config_widget.py,sha256=XgSqqnF9j2Gwfk2lOBPrWIEbtRwR-nDdhO7GOVFTvV8,7835
-AMS_BP/gui/widgets/channel_config_widget.py,sha256=WvsoV7iNaY4T9dl3QL-kqCXNKJOWbkWK5w7BqUpVDpM,10780
-AMS_BP/gui/widgets/condensate_config_widget.py,sha256=YI_LZJ_EP73SsFvTdoWjqnE2e0_XLv02Gth1MErc8oM,12128
-AMS_BP/gui/widgets/experiment_config_widget.py,sha256=1FdSIp6lO-Gscd98prGv7MCL-dziklIaN62TwQYNJ6M,9286
-AMS_BP/gui/widgets/flurophore_config_widget.py,sha256=Bri9TttiYM7eBkrcxLVjjvhein5FEsxuz2FYJvcvW1I,19682
+AMS_BP/gui/widgets/camera_config_widget.py,sha256=pYzSSNUBzo2TFzw3qwSW-PuduD6M3q4XqDCGZJpdUWs,7787
+AMS_BP/gui/widgets/cell_config_widget.py,sha256=rNQljIob3oUGa02bKiG9kxHWlE2-o30gEH4oUv43Msg,8062
+AMS_BP/gui/widgets/channel_config_widget.py,sha256=zBfP9xySSqBQWSyXyaGqPViTHJhQKCen6gMcLl9Tgx0,11007
+AMS_BP/gui/widgets/condensate_config_widget.py,sha256=K2sYIHhXbqmpDf6edWaxnYVYEjDYffciucN7XivJc8M,12573
+AMS_BP/gui/widgets/experiment_config_widget.py,sha256=Oa_3XvzOk3TmFdQ0LmOLdq8P8kRb6HVwc-ypw7YFq78,9815
+AMS_BP/gui/widgets/flurophore_config_widget.py,sha256=jOWwo7hmX7b_fNcbaTbHLfaoKTivvdiq8-yHs2b8198,19897
 AMS_BP/gui/widgets/general_config_widget.py,sha256=YbnE11TnWZBgb-xqKWM00p8RdSp-9eTbwTZ9mikPvZc,1321
-AMS_BP/gui/widgets/global_config_widget.py,sha256=6X-NrBz5qc2mfDnH0kBGQKTgBaI3hqaaOAMpegFM7hs,4881
-AMS_BP/gui/widgets/laser_config_widget.py,sha256=gtaZdFsPh8Zai03IoyhSp95hXa6biAoFmhJMaSe38XM,8737
-AMS_BP/gui/widgets/molecule_config_widget.py,sha256=3EaE2iPfelxtvrA0QgF1lJ06KZ0Dh1VVje_oT1Df-2o,27789
+AMS_BP/gui/widgets/global_config_widget.py,sha256=QqkJiPFZfe73a1fbgf6oCmLacbp3Cda7UH4lr0A3rXo,5098
+AMS_BP/gui/widgets/laser_config_widget.py,sha256=oqINXtRUhVzwW4HE9jsHcFWVp3q5n4RBlXumdZZoHjM,8964
+AMS_BP/gui/widgets/molecule_config_widget.py,sha256=Bog31_wjTJ0uyw4qpL_3m8EK7jlc3GNMgn-7EOS-k0g,28063
 AMS_BP/gui/widgets/output_config_widget.py,sha256=pExiAHIHs0-J-dY2lZtfB0ei9oNjZIJKDQtWDSjFZOY,2105
 AMS_BP/gui/widgets/psf_config_widget.py,sha256=75ggeolYI_Sbn5LD_hUGY3S4Z9uRkJGtzZhb79NgsY4,4534
 AMS_BP/gui/widgets/utility_widgets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 AMS_BP/gui/widgets/utility_widgets/scinotation_widget.py,sha256=sLrQqueRJ0wEy4aF1I8UJO0Bolnm7yTsAyfNqrHiAKI,553
 AMS_BP/gui/widgets/utility_widgets/spectrum_widget.py,sha256=QQjYV-aErjyI1HdOZMIPaddHpi0sag6r4V8nBSdgEn8,3659
+AMS_BP/gui/widgets/utility_widgets/toggleswitch_widget.py,sha256=vldANnsLcoqwmM8PNQc6PZAMtPN2h6A-JCCx9etBLKU,1945
 AMS_BP/logging/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 AMS_BP/logging/logutil.py,sha256=HkkB0mF8SL68gmJcOngBppNi6InX18Goxro5LJR-inA,2420
 AMS_BP/logging/setup_run_directory.py,sha256=B9sG_N3lOya_gVaJTs7GDVXpTY1Ov3jMPGTj2ttydM0,897
@@ -96,8 +99,8 @@ AMS_BP/utils/decorators.py,sha256=4qFdvzPJne0dhkhD1znPxRln1Rfr5NX8rdcCDcbATRU,62
 AMS_BP/utils/errors.py,sha256=7BOd-L4_YeKmWn3Q4EOdTnNF3Bj_exDa3eg5X0yCZrc,759
 AMS_BP/utils/maskMaker.py,sha256=2ca3n2nc8rFtUh1LurKXOJJsUmhrOpWbRnVX7fjRVvs,335
 AMS_BP/utils/util_functions.py,sha256=9Qlr4kjY04fObktR8TrzB0IgoG1yXtcmxPRX9AN34mM,9671
-ams_bp-0.4.0.dist-info/METADATA,sha256=lIZpclOoeyFhFZ5eMzXolrDtIj2V1q9W0nJHAHXqWjQ,10397
-ams_bp-0.4.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ams_bp-0.4.0.dist-info/entry_points.txt,sha256=06NS85P4dz6vosMOKXHfx8l7gK9WXBZxuwjl55XfT2c,65
-ams_bp-0.4.0.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
-ams_bp-0.4.0.dist-info/RECORD,,
+ams_bp-0.4.3.dist-info/METADATA,sha256=tsHlRpGj25zeFtHI46UbcCRm73MRIiBXIU8MpD2ogxA,9593
+ams_bp-0.4.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ams_bp-0.4.3.dist-info/entry_points.txt,sha256=06NS85P4dz6vosMOKXHfx8l7gK9WXBZxuwjl55XfT2c,65
+ams_bp-0.4.3.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
+ams_bp-0.4.3.dist-info/RECORD,,